Notes for Authors Notes for Authors

notes for authors

Notes for authors

1. Aims and scope 2.3. Scientific Comment Acta Crystallographica Section F is a rapid structural biology Comments of general scientific interest to the readership are communications journal. welcomed. These should not normally exceed two journal pages and Articles on any aspect of structural biology, including structures should be submitted as in x3. determined using high-throughput methods or from iterative studies such as those used in the pharmaceutical industry, are welcomed by 2.4. Special issues the journal. Acta Cryst. F also publishes special sections and issues devoted to The journal offers the option of open access, and all communica- the work of groups focusing on specific areas of structural biology. tions benefit from unlimited free use of colour illustrations and no For more information, contact [email protected]. page charges. Authors are encouraged to submit multimedia content for publication with their articles. Acta Cryst. F has a dedicated online tool called publBio that is 3. Submission and handling of articles designed to make the preparation and submission of articles easier for authors. 3.1. Submission Articles must be submitted electronically via the web at http:// journals.iucr.org/f/services/submit.html or via publBio at http:// publbio.iucr.org. 2. Categories of contributions Full details of the submission procedure, instructions for submitting an article and details of the files required are given at Contributions should conform to the general editorial style of the http://journals.iucr.org/f/services/submitinstructions.html. All authors journal. Articles should not exceed four journal pages (about 3000 are encouraged to use the publBio publication tool to prepare words) and structural communications should describe a single and submit their article (see http://journals.iucr.org/f/services/ structure. Typical articles may be viewed by going to http:// publbiosubmission.html). Alternatively, authors may use the Word or journals.iucr.org/f/sample_issue.html. OpenOffice templates available from http://journals.iucr.org/services/ docxtemplate/. Authors of structural articles are required to provide a wwPDB 2.1. Research Communications validation report on submission. These are short focused articles and can describe any aspect of Articles describing the crystallization of a biological macro- structural biology. publBio templates are available for this type of molecule must be prepared using publBio or the publBio tools within article (see x3.1). the IUCr Word template. Full details of how to submit articles For articles that describe the determination of biological structures, using publBio can be found at http://journals.iucr.org/f/services/ details of data requirements can be found at http://journals.iucr.org/f/ publbiosubmission.html. services/evaluationcriteria/. The contact author must provide an e-mail address for all editorial Articles describing the crystallization of a biological macro- communications and despatch of proofs and electronic reprints. molecule should describe more than just a routine crystallization and should include novel aspects of the crystallization procedure together 3.2. File format with new science. They should cover expression, purification and For articles not produced using publBio, the text, tables, figures crystallization of a macromolecule, and the validation of crystal and figure captions should be supplied as a single file in Word or quality, including a presentation of the diffraction data statistics. OpenOffice format. For all articles, each figure or scheme should also Evidence of the identity of the crystallized macromolecule is also be provided as a high-resolution graphics file (minimum 600 d.p.i.) in required. Special submission instructions apply to this type of article TIFF, PostScript, encapsulated PostScript or PNG format. Supporting (see x3.1) information should be provided at the end of the article or in one of Brief descriptions of special methods, equipment modifications, the formats listed at http://journals.iucr.org/services/filetypes.html. techniques for accomplishing certain tasks etc. related to crystallization or other fields of structural biology are also welcomed. 3.3. Handling of articles Each article is handled by an editor chosen by the author from a list of those available at the time of submission. Authors should 2.2. Letters to the Editor choose an editor whose area of expertise most closely matches the These may deal with any aspect of crystallography, its role, its subject of the article. Details of the current Editorial Board can be propagation or the proper function of its Societies etc. They may also found at http://journals.iucr.org/f/services/editors.html. deal with a technical or scientific observation that would usefully be All contributions will be seen by referees (normally two) before brought to a wider audience. Letters should be submitted to one of they can be accepted for publication. The editor to whom the the Section Editors. manuscript is assigned is responsible for the review process and notes for authors for accepting or rejecting the article. This responsibility includes 3.5. Author grievance procedure decisions on the final form of the article and interpretation of An author who believes that an article has been unjustifiably these Notes when necessary. Further information on the peer treated by the Co-editor may appeal initially to the Section Editors review process can be found at http://journals.iucr.org/f/services/ for a new review and, finally, to the Editor-in-chief of Acta Crystal- peerreview.html. lographica if the author is still aggrieved by the decision. The initial Changes to an article requested by the Section Editors, Co-editor appeal must be made within three months of rejection of the article. or the editorial staff should be received within one month of trans- The decision of the Editor-in-chief is final. mittal to the author, otherwise the submission will be considered as withdrawn. If an article is not acceptable after two revisions it will not be considered further. Any subsequent communication of the mate- 3.6. Copyright rial will be treated as a new submission in the editorial process. An Except as required otherwise by national laws, an author will be article that has been rejected must not be resubmitted to any IUCr required to agree to the transfer of copyright before an article can be journal unless the reasons given for the rejection have been fully accepted. Authors selecting open access do not need to transfer addressed in the revised version. copyright. Details of author rights can be found at http:// After initial submission, any revised or new files should be journals.iucr.org/services/authorrights.html. uploaded only in response to a specific request from an editor. For accepted articles, it is the responsibility of the Managing Editor 3.7. Open access to prepare the article for publication. This may involve correspondence with the authors and/or the responsible editor in order to Authors are given the opportunity to make their articles ‘open resolve ambiguities or to obtain satisfactory figures or tables. The access’ on Crystallography Journals Online. Authors of open-access date of acceptance that will appear on the published article is the date articles will not be asked to transfer copyright to the IUCr, but will on which the Managing Editor receives the last item required. instead be asked to agree to an open-access licence. This licence is Correspondence will be sent to the contact author who submitted the identical to the Creative Commons Attribution (CC-BY) Licence. article unless the Managing Editor is informed of some other suitable Further details can be found at http://journals.iucr.org/services/ arrangement. Contact details for the Managing Editor of Section F openaccess.html. can be found at http://journals.iucr.org/services/contactus.html. On rare occasions, an editor may consider that an article is better 3.8. Publication fees suited to a section of Acta Crystallographica other than that specified There are no fees for colour figures or electronic reprints. If by the author(s), to IUCrJ, Journal of Applied Crystallography or to authors require open access or printed reprints there is a charge and Journal of Synchrotron Radiation. Any change to the section or details will be given at the proof stage. journal of publication will only be made after full discussion with the contact author. Articles will be checked for plagiarism using the CrossCheck service. 4. Article preparation 4.1. General information Before preparing articles, authors should consult a current issue of 3.4. Author’s warranty the journal to make themselves familiar with the general format, such as the use of headings, layout of tables and citation of The submission of an article is taken as an implicit guarantee that references. A sample issue is available at http://journals.iucr.org/f/ the work is original, that it is the author(s) own work, that all authors sample_issue.html. are aware of and concur with the submission, that all workers All contributions must be accompanied by an English language involved in the study are listed as authors or given proper credit in Abstract and a one or two sentence Synopsis of the main findings of the acknowledgements, that the article has not already been the article for inclusion in the Table of Contents. Authors should also published (in any language or medium), and that it is not being supply at least five keywords. considered and will not be offered elsewhere while under consid- The Abstract should state as specifically and as quantitatively as eration for an IUCr journal. The inclusion of material in an informal possible the principal results obtained. It should be suitable for publication, e.g. a preprint server or a newsletter, does not preclude reproduction by abstracting services without a change in wording and publication in an IUCr journal. should not repeat information given in the title. It should make no The co-authors of an article should be all those persons who have reference to tables, diagrams, atom numbers or formulae contained in made significant scientific contributions to the work reported, the article. It should not contain footnotes and should not include the including the ideas and their execution, and who share responsibility use of ‘we’ or ‘I’. and accountability for the results. Other contributions should be Research communications should normally be divided into the indicated in the acknowledgments. Changes to the list of authors will following sections: introduction, experimental (including materials normally require the agreement of the editor and all authors. and methods), results, discussion, acknowledgements and references. The IUCr is a member of COPE (Committee on Publication Ethics) and endorses its recommendations, including the Code of Conduct for Editors, which are available at http://www. 4.2. Quality of writing publicationethics.org/. Important considerations related to publica- Articles should be clearly written and grammatically correct. If the tion have been given in the ethical guidelines published in Acc. Chem. Co-editor concludes that language problems would place an undue Res. (2002), 35, 74–76 and Graf et al. [Int. J. Clin. Pract. (2007), burden on the referees, the manuscript may be returned to the 61(Suppl. 152), 1–26]. Authors are expected to comply with these authors without review. Details of language-editing services can be guidelines. found at http://journals.iucr.org/services/languageservices.html. notes for authors

4.3. Diagrams and photographs (‘figures’) 4.5. Video and multimedia content A set of guidelines for preparing figures is available from http:// Multimedia content (e.g. time-lapse sequences, three-dimensional journals.iucr.org/f/services/help/artwork/guide.html. Figures should structures) is welcomed. For details of how to prepare enhanced be prepared using one of the file formats listed in x3.2. three-dimensional figures, see x4.3.8. The preferred file formats The choice of figures should be optimized to produce the shortest for multimedia are given at http://journals.iucr.org/services/ article consistent with clarity. Duplicate presentation of the same filetypes.html. information in both figures and tables is to be avoided, as is redun- dancy with the text. Supplementary figures may be deposited (see x6). An illustration for the first page of the article and the contents pages may be included. 4.6. Mathematics and letter symbols 4.3.1. Quality. Electronic files in the formats listed in x3.3 are Authors submitting in Word should use the Word equation editor essential for high-quality reproduction. The resolution of bitmap to prepare displayed mathematical equations. graphics should be a minimum of 600 d.p.i. The use of the stop (period) to denote multiplication should be 4.3.2. Size. Diagrams will normally be sized so that the greatest avoided except in scalar products. Generally no sign is required but, width including lettering is less than the width of a column in the when one is, a multiplication sign () should be used. journal (8.8 cm). Scalar variables and non-standard functions should appear in italic 4.3.3. Lettering and symbols. Fine-scale details and lettering must type. be large enough to be clearly legible (ideally 1.5–3 mm in height) Vectors should be in bold type and tensors should be in bold-italic after the whole diagram has been reduced to one column width. type. Lettering should be kept to a minimum; descriptive matter should Greek letters should not be spelled out. be placed in the caption. Care should be taken not to cause confusion by using the same 4.3.4. Numbering and captions. Diagrams should be numbered in letter symbol in two different meanings. a single series in the order in which they are referred to in the text. Gothic, script or other unusual lettering should be avoided. Each figure should be accompanied by a caption. Another typeface may be substituted if that used by the author is not 4.3.5. Stereofigures. Atom labelling when included should be on readily available. both left and right views in stereo perspective. Both views should be All displayed equations, including those in published Appendices, incorporated into a single figure. The type of stereoview used (cross- should be numbered in a single series. eyed or wall-eyed) should be given in the caption. 4.3.6. Colour figures. Figures in colour are accepted at no cost to the author. Authors preparing colour figures should consider how the figure would look in greyscale and to readers who are colour-blind. It 4.7. Nomenclature is very important that poor contrast (e.g. pale colours with a white background) be avoided. 4.7.1. Units. The International System of Units (SI) is used except ˚ 10 4.3.7. Cover figure. Authors are encouraged to supply suggestions that the a˚ngstro¨m (symbol A, defined as 10 m) is generally for the cover illustration. Authors who supply an mmCIF with their preferred to the nanometre (nm) or picometre (pm) as the appro- submission and/or use the interactive tool in described in x4.3.8 may priate unit of length. Recommended prefixes of decimal multiples n have their structure considered for an animated cover. should be used rather than ‘ 10 ’. 4.3.8. Enhanced figures. An online tool for authors to prepare 4.7.2. Biochemical nomenclature. The recommendations of the standard and corresponding three-dimensional interactive structural Nomenclature Committee of IUBMB and the IUPAC-IUBMB Joint diagrams is available from http://submission.iucr.org/jtkt. Commission on Biochemical Nomenclature (see http://www.chem. qmul.ac.uk/iubmb/) should be followed as far as practicable. The recommendations of the latest edition of Enzyme Nomenclature (1992, San Diego: Academic Press; and its supplements) should be 4.4. Tables followed as far as possible (see http://www.chem.qmul.ac.uk/iubmb/ Authors submitting in Word should use the Word table editor to enzyme). This includes the quoting of EC numbers. It is recom- prepare tables. Experimental tables should be prepared as in x4.4.3 mended that authors use the new nomenclature for restriction below. enzymes, DNA, methyltransferases, homing endonucleases (and their 4.4.1. Use of tables. Extensive numerical information is generally genes) that has been proposed by Roberts et al. [(2003), Nucleic Acids most economically presented in tables. Text and diagrams should not Res. 31, 1805–1812]. be redundant with the tables. 4.7.3. Crystallographic nomenclature. Authors should follow the 4.4.2. Design, numbering and size. Tables should be numbered in a general recommendations produced by the IUCr Commission on single series of arabic numerals in the order in which they are referred Crystallographic Nomenclature (see reports at http://www.iucr.org/ to in the text. They should be provided with a caption. iucr/commissions/cnom.html). Quality indicators should be given as Tables should be carefully designed to occupy a minimum of space defined in H. M. Einspahr & M. S. Weiss (2011). International Tables consistent with clarity. for Crystallography, Vol. F, ch. 2.2, pp. 64–74. 4.4.3. Experimental tables. Each article describing the crystal- 4.7.4. Nomenclature of chemical compounds etc. Formulae and lization or structure determination of a macromolecule will normally nomenclature should conform to the rules of nomenclature estab- include a standard experimental details table. Authors should use lished by the International Union of Pure and Applied Chemistry publBio to generate this table. The tool can be found at http:// (IUPAC) and other appropriate bodies. As far as possible the crys- publbio.iucr.org. Alternatively, a standard experimental table should tallographic nomenclature should correspond to the systematic name. be generated using the table tools within the IUCr Word template Any accepted trivial or non-systematic name may be retained, but available from http://journals.iucr.org/services/docxtemplate/. the corresponding systematic (IUPAC) name should also be given. notes for authors

4.8. References should also contain additional proof that the correct macromolecule References to published work must be indicated by giving the has been crystallized (e.g. SDS–PAGE, mass spectrometry or N- authors’ names followed immediately by the year of publication, e.g. terminal sequencing of dissolved crystals) and enough new infor- Neder & Schulz (1998) or (Neder & Schulz, 1998). Where there are mation to be acceptable. If the target sequence has between 40% and three or more authors the reference in the text should be indicated in 80% sequence identity to the closest homologue, additional infor- the form Smith et al. (1998) or (Smith et al., 1998) etc. mation, such as enzyme kinetics or binding studies data, is required. If The reference list should be arranged alphabetically and conform the sequence identity is greater than 80%, the article will, in general, with the following style: not be acceptable unless there is some novelty in the crystallization experiment, e.g. a special procedure, special seeding or a novel Bru¨nger, A. T. (1992a). X-PLOR. Version 3.1. A System for X-ray compound. Crystallography and NMR. Yale University, Connecticut, USA. Bru¨nger, A. T. (1992b). Nature (London), 355, 472–474. 5.3. NMR data Bru¨nger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, Guidelines for publication of NMR data are available from http:// N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). journals.iucr.org/services/nmr/. Acta Cryst. D54, 905–921. Crowther, R. A. (1972). The Molecular Replacement Method, edited by 5.4. Neutron data M. G. Rossmann, pp. 173–178. New York: Gordon and Breach. International Union of Crystallography (2014). (IUCr) Structural In articles reporting neutron data, preliminary nuclear density Biology Communications, http://journals.iucr.org/f/journalhomepage.html. maps should not be included unless the relevant statistics of R, Rfree, Jones, A. B. (2015). Acta Cryst. F71. In the press. correlation coefficient and error estimates are provided. Schomaker, V. (1946). Personal communication. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. 5.5. Small-angle scattering data Weiss, M. S., Einspahr, H., Baker, E. N., Dauter, Z., Kaysser-Pyzalla, A., Kostorz, G. & Larsen, S. (2010). Acta Cryst. F66, doi:10.1107/ Guidelines for articles reporting structural modelling of small- S1744309110041825. angle scattering may be found at http://journals.iucr.org/services/sas/. Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., For articles that present experimental SAS data, the deposition of an Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, ASCII file representing the background-corrected scattering A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., profile(s) with errors is required. Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235–242. 5.6. Validation reports Note that all authors and inclusive page numbers must be given. Authors of structural articles are required to provide a validation References in the journal will be linked, where possible, to the report on submission. Authors are encouraged to presubmit their original publication and also to appropriate bibliographic databases data to the wwPDB and obtain a validation report for their structure. (e.g. Medline). Further information about validation reports can be found in the Citations in supporting information should appear in the main online submission instructions. body of the article or be given in a related literature section. 4.8.1. References to structures. Identification of individual structures in the article by use of database reference (identification) codes 6. Supporting information should be accompanied by a full citation of the original literature in 6.1. Purpose and scope the reference list. In such cases, the citation in the text should take the Supporting information (such as experimental data, additional form ‘ ...the structure of amicyanin (PDB code 1aac, Cunane et al., figures and multimedia content) that may be of use or interest to 1996)’. some readers but does not form part of the article itself will be made available from the IUCr archive. Arrangements have also been made 5. Evaluation criteria for such information to be deposited, where appropriate, with other 5.1. Structural data relevant databases. Evaluation criteria and data recommended for inclusion in articles describing the structure determination of a macromolecule can be 6.2. IUCr archive found at http://journals.iucr.org/f/services/evaluationcriteria/. All material for deposition in the IUCr archive should be supplied For review purposes, authors of structural articles may be asked by in one of the formats described at http://journals.iucr.org/services/ the Co-editor to submit the coordinate file of the structure described filetypes.html.. in the paper together with the structure-factor amplitudes used for refinement. 6.3. Macromolecular structures Authors should follow the deposition recommendations of the 5.2. Crystallization data IUCr Commission on Biological Macromolecules [Acta Cryst. (2000), A list of data recommended for inclusion in articles describing the D56, 2]. For all structural studies of macromolecules, coordinates and crystallization of a macromolecule can be found at http://journals. the related experimental data (structure-factor amplitudes/inten- iucr.org/f/services/evaluationcriteria/. Before submission, authors sities) must be deposited at a member site of the Worldwide Protein should perform a sequence search against the Protein Data Bank and Data Bank (http://www.wwpdb.org) if a total molecular structure has the closest homologue should be mentioned in the article. The been reported. Authors are encouraged to deposit their data with the author’s sequence is expected to have 40% or less identity to the wwPDB in advance of submission to the journal and to provide an closest homologue (or have other interesting features). The article mmCIF and a wwPDB validation report which will be required on notes for authors submission. Further information about mmCIFs and validation A toolkit for preparing enhanced figures is available at http:// reports can be found in the online submission instructions. Authors submission.iucr.org/jtkt. must supply the wwPDB reference codes before the article can be published and the data must be released upon publication. 7.2. Status information For NMR structures, in addition to the coordinates, assigned Authors may obtain information about the current status of their chemical shifts and the restraint data used in the last round of articles at http://journals.iucr.org/services/status.html. refinement should be deposited with the wwPDB. It is recommended that the NOE peak list also be deposited. 7.3. Proofs Authors are encouraged to make arrangements for the diffraction data images for their structure to be archived and available on Proofs will be provided in portable document format (pdf). The request. contact author will be notified by e-mail when the proofs are ready for downloading.

7.4. Reprints 7. Author information and services After publication, the contact author will be able to download the An author services page is available at http://journals.iucr.org/f/ electronic reprint of the published article, free of charge. services/authorservices.html. 7.5. Open-access articles

7.1. Author tools The final published version of each IUCr open-access article is deposited with PubMed Central on behalf of the authors. A number of tools are available to help with the preparation of articles. 7.6. Publicising your article Authors are encouraged to use publBio available at http:// publbio.iucr.org. This web service provides a quick and easy route to There are many ways in which the IUCr promotes and raises prepare and submit an article, and helps to ensure that all items awareness of articles published in its journals. More information on necessary for publication are included. this and suggestions on how to publicise your articles can be found at Alternatively, Word and OpenOffice templates can be downloaded http://journals.iucr.org/f/services/articlepublicity.html. from http://journals.iucr.org/services/helpsubmit.html/. Table tools within the Word template can be used to prepare 7.7. Crystallography Journals Online experimental tables from an mmCIF file or from a structure in the All IUCr journals are available on the web via Crystallography PDB. Journals Online; http://journals.iucr.org/.